Environmental activist group the Sea Shepherd Conservation Society says it is chasing two illegal fishing boats that were spotted sailing just 50 nautical miles from Australia's Mawson Base in Antarctica.

He said the ships were close to Australia's Mawson station on Tuesday morning but they were not fishing at the time.

"The decks of both the vessels are loaded with gill netting gear, which is a banned fishing method inside the ... region," said Mr Chakravarty.

"[They were] discharging fish offal and guts over the side as well which would indicate that the vessels had recently been engaged in fishing operations and are probably cleaning their decks and storing the fish taken illegally into their freezers."

Sea Shepherd said it believed the true owner of the boat was a Spanish syndicate.

Australia urged to deploy Customs vessel Ocean Shied

The New Zealand government said it was pursuing the matter with the Spanish government to try to find out if the owners of the boat are based in Spain and can be prosecuted there.

Mr Chakravarty said Sea Shepherd was planning to take action in the Southern Ocean to stop the illegal fishing.

"I'll be using the Sam Simon directly as a blockading tool and putting my vessel behind these fishing vessels where they run their fishing gear out from and that should pretty quickly end their fishing operations," he said.

Tasmanian Greens senator Peter Whish-Wilson called on the Federal Government to send a Customs ship down to the Southern Ocean to intercept the illegal fishing boats.

"The Ocean Shield was promised by the Liberal government in opposition," he said.

"[A] promise that they would send this customs vessel down to patrol the Southern Ocean.

"They've recently reiterated that promise; they said there'd be two 40-day patrols to patrol for unregulated illegal fishing.

"They need to send that boat immediately."

A specialist in Antarctic policy at the University of Tasmania, Julia Jabour, said while Australia claimed sovereignty over the waters that the ships were in, not many other countries recognised the claim.

"Sea Shepherd in their press release have suggested or in fact criticised the Australian Government for not responding to the presence of these vessels in Australian waters and I'd like to reiterate that they are not Australian waters," she said.

"But if they had been, for example, another couple of hundred nautical miles north and were in fact in Heard Island or the McDonald Island exclusive economic zone, which is without a doubt Australian water, then you would see a response from Australia.

"But the Australian Government is not doing nothing, simply because there is nothing they can do."

A spokesman for Border Protection Minister Peter Dutton said Customs patrols were conducted based on ongoing assessments of operational priorities across all maritime security threats.

He said they could not say when or if a patrol was being sent to the Southern Ocean because of what the Minister's office calls "operational security purposes".